Amino Acids
Amino acids (such as proline
below) are the basic units from
which proteins are made.
Plants can manufacture all the amino acids
they require, but animals must obtain a
certain number of ready-made essential
amino acids from their diet.
All other amino acids can be constructed
from these essential amino acids.
The order in which the different amino
acids are linked together to form
proteins is controlled by genes on the
chromosomes.
Glu
Amino acids link
together (right) to
form proteins.
Phe
Tyr
Ser
Iso
Met
Ala
Ala
Ser
Amino Acids
There are approximately 20 different
amino acids acids found in proteins.
The “R” group varies in
chemical make-up with
each type of amino acid
All amino acids have a common
structure:
The ‘R’ group is variable, which
means that it is different in each
amino acid.
R
NH2
C
Amine
group
H
Hydrogen
atom
Carbon
atom
COOH
Carboxyl group
makes the molecule
behave like a weak
acid
Amino Acids
The ‘R’ groups of amino acids can have quite
diverse chemical properties.
This “R” group can form
disulfide bridges with other
cysteines to create cross
linkages in a polypeptide chain.
This “R” group gives
the amino acid
alkaline properties.
This “R” group gives
the amino acid
acidic properties.
NH2
CH2
CH2
CH2
CH2
SH
CH2
NH2
C
H
Cysteine
COOH
NH2
C
COOH
CH2
COOH
NH2
C
COOH
H
H
Lysine
Aspartic acid
Amino Acids
Not all amino acids can be manufactured by our body.
Ten must be obtained from our diet. These are called essential amino acids.
The essential amino acids are marked by ◆
Amino acids occurring in proteins
Alanine
Glycine
Proline
Arginine
◆Histidine
Serine
Asparagine
◆Isoleucine
◆Threonine
Aspartic acid
◆Leucine
◆Tryptophan
Cysteine
◆Lysine
◆Tyrosine
Glutamine
◆Methionine
◆Valine
Glutamic acid
◆Phenylalanine
Polypeptides
A polypeptide chain is formed when amino acids are linked together via peptide
bonds to form long chains.
The process of joining amino acids is called condensation.
A polypeptide chain may contain several hundred amino acids.
A polypeptide chain may be functional by itself, or may need to be joined to
other polypeptide chains to become functional.
Peptide
bond
Peptide
bond
Peptide
bond
The diagram above represents a polypeptide chain.
The peptide bonds between amino acids are
indicated with arrows.
Peptide
bond
Condensation & Hydrolysis
Two amino
acids
Condensation
Amino acids are joined together to
form peptide or polypeptide chains.
Polypeptide chains are broken
down into smaller peptide chains or
simple amino acids.
A water molecule provides a
hydrogen and hydroxyl group.
Hydrolysis
Hydrolysis
Condensation
A water molecule is released.
Peptide
bond
Example: digestion
Dipeptide + H2O
H2O
Condensation & Hydrolysis
H
Two
amino
acids
R
N
H
C
O
H
C
N
OH
H
R
H
C
Dipeptide +
water
N
H
C
OH
H
Condensation
H
O
Hydrolysis
R
O
H
R
C
C
N
C
H
H
O
C
+ H2O
OH
Proteins
Proteins are macromolecules, consisting of many amino acids linked
together as polypeptide chains.
Each cell contains several hundred to several thousand proteins.
Proteins play a key role in the body. They are involved in:
Enzyme reactions
Human Cytochrome C
(respiratory chain)
Oxidation-reductions, e.g. respiratory chain
Structure
Storage
Transport
Cell signaling
Defense
Insulin-like growth factor 1
(used in cell signaling)
These two proteins are depicted
as 3D cartoon and stick models.
Protein Structure
The conformation (or shape) a protein takes is
dependent upon the protein’s amino acid
sequence.
The “R” groups of each amino acid react and
interact with each other. These interactions
determine the final conformation of the
protein.
A protein’s conformation is central to its function.
Lysozyme is a single polypeptide
strand of 129 amino acids and a
tertiary structure which is part αhelix, part β- sheet and part
irregular sections.
If the shape is altered then the protein may no
longer be able to perform its biological role.
Proteins have up to four levels of structure:
primary: the linking of amino acids in the
polypeptide chain.
secondary: the shape of the polypeptide chain
tertiary: the fold of the polypeptide chain
quaternary: the interaction of two or more
polypeptide chains
Hemoglobin has a
complex quaternary
structure with four subunits
Proteins:
Primary Structure
Phe
Glu
Tyr
Ser
The primary (1°) protein structure is
the amino acid sequence.
Iso
Hundreds of amino acids link
together to form polypeptide chains.
Phe
The chemical interaction (attraction
and repulsion) of the individual
amino acids helps define the final
protein shape.
Ala
Glu
Met
Gly
Ala
When amino acids are
linked together they form a
polypeptide chain.
Ala
b
Proteins:
Secondary Structure
The secondary (2°) structure is the
shape of the polypeptides chain.
There are two common types of
secondary structure:
Hydrogen
bonds
α-helix coil
β-pleated sheets
Most proteins, e.g. lysozyme, contain
a mixture of the two secondary
structures, but the levels of each vary.
Two peptide
chains
Secondary structures are a result of
hydrogen bond interaction between
neighboring CO and NH groups of the
polypeptide backbone.
α-helix
β-pleated sheet
Proteins:
Tertiary Structure
The tertiary (3°) structure of a
protein is the way in which it is
folded (called its fold).
Heme group
The protein folds because of
interactions between the “R”
groups, or side chains on the
amino acids. Several interactions
may be involved:
Disulfide bonding (reactions
between two cysteine amino acids).
These form the strongest links.
Weak bonding (ionic and hydrogen).
Hydrophobic interactions.
The tertiary structure of a
hemoglobin molecule shows it is
folded around a heme group which
binds oxygen. Disulphide bridges
help maintain the structure.
Disulfide bridge
Proteins:
Quaternary Structure
Some proteins contain more than one polypeptide chain.
The polypeptide chains, or subunits, aggregate together to become a functional unit.
The aggregation of subunits is called the quaternary (4°) structure of a protein.
Alpha chain
Beta chain
The hemoglobin molecule
has four subunits: two alpha
chains and two beta chains.
At the core of each subunit is an
iron containing heme group,
which binds oxygen.
Heme group
Protein Structure:
Overview
1
° Glu
Ser
Glu
Tyr
Ala
Iso
Gly
Phe
Met
There are four levels of protein structure:
Phe
Ala
Primary structure (1°): The sequence of
amino acids in a polypeptide chain.
Secondary structure (2°): The shape of the
polypeptide chain (e.g. alpha-helix).
Ala
2
°
Tertiary structure (3°): The overall
conformation (shape) of the
polypeptide caused by folding.
Quaternary structure (4°): The association
of multiple subunits of polypeptide chains.
4
°
3°
Categorizing Proteins
Proteins can be categorized according
to their tertiary structure:
Globular proteins
Fibrous proteins
disulfide
bond
α-chain
Fibers form due
to cross links
between collagen
molecules
ϐ-chain
Bovine insulin (above) is an example
of a small globular protein. It consists
of two chains held together by
disulfide bridges between neighboring
cysteine (Cys) molecules.
Collagen (above) is an example of a fibrous
protein. It consists of three α helical
polypeptide chains wound around each
other. Hydrogen bonding between glycine
residues holds these chains together.
Globular Proteins
Globular proteins are very diverse in their
structure.
subunit
They can exist as single chains or comprise several
chains, as occurs in hemoglobin and insulin.
Properties of globular proteins:
subunit
Easily soluble in water
subunit
Tertiary structure is critical to function
Polypeptide chains are folded into a spherical shape
Functions of globular proteins:
subunit
Catalytic, e.g. enzymes
Regulatory, e.g. hormones
Transport, e.g. hemoglobin
Protective, e.g. antibodies
Hemoglobin (above) is a globular protein.
Its heme (iron containing) groups bind
oxygen. The red blood cells which transport
oxygen around the body are mostly made
up of hemoglobin.
Fibrous Proteins
Fibrous proteins form long shapes,
and are only found in animals.
Properties of fibrous proteins:
Water insoluble
Very tough physically; they may be supple or
stretchy
Parallel polypeptide chains in long fibers or sheets
Functions of fibrous proteins:
Structural role in cells and organisms, e.g.
collagen in connective tissue, bones,
tendons
Contractile, e.g. myosin, actin
Fibrous proteins (such as collagen
above) often form aggregates because
of their hydrophobic properties.
Collagen makes up about 25% of total
protein in mammals, making it the most
abundantly occurring protein.
Protein Function
Proteins can be classified according to their functional role in an organism.
Hemoglobin
Function
Examples
Structural
Forming the structural components of
tissues and organs
Collagen, keratin
Regulatory
Regulating cellular function (hormones,
cell signaling)
insulin, glucagon, adrenalin, human
growth hormone, follicle stimulating
hormone
Contractile
Forming the contractile elements in
muscle (skeletal, smooth, cardiac)
myosin, actin
Immunological
Functioning to combat invading
microbes
antibodies such as gammaglobulin
Transport
Acting as carrier molecules
hemoglobin, myoglobin
Catalytic
Catalyzing metabolic reactions
(enzymes)
amylase, lipase, lactase, trypsin